A "hidden directory" is the given name to any folder that was made by a user, but will not be shown up on the dashboard. To make such a folder, a user must select the "New Folder" button and type in any name that starts with a period ("."), once this is done, the folder will have been made, however, the only way the owner of a website can view the directory via the dashboard is to manually enter the URL of the folder, the URL should look something like this;
As you cannot normally view the folder via the dashboard, it is impossible to delete the folder.
All files (HTML, PNG, MP3, etc) on such folders will be treated the same as they would on any other folder, however, the site owner will be unable to edit the files via the online editor as it will keep on showing "Loading..." forever.
A live example of such a directory can be found here: https://thewikion.neocities.org/.hidden/